From March 5, 1913 to February 10, 1916, Garrison served as Secretary of War in the Wilson administration. Garrison and Wilson never fit well together. Garrison was much more willing to intervene militarily overseas than was the President. This was especially evident in regard to Mexico. Garrison urged American intervention into the Mexican revolution to restore order. During the Preparedness campaign of 1916, when Wilson was trying to convince Congress to raise military spending, Garrison supported a plan for expanding the US military with what he called the Continental Army Plan. Garrison's proposal would establish a standing army of 140,000 and a national, volunteer reserve force of 400,000 men. Wilson initially gave the plan tepid support, but Garrison ran into opposition from both those who felt his plan went too far in creating a large standing army, as well as from those who felt it did not go far enough. Wilson was convinced by allies in Congress to back an alternative plan which emphasized not Garrison's national volunteer force, but a continued role for the states' National Guard. Garrison resigned in February 1916 over these differences.[3]

After leaving Wilson's administration Garrison returned to the practice of law in the firm of Hornblower, Miller & Garrison. He was appointed receiver of the Brooklyn Rapid Transit Company in December 1918 and served until June 1923. He died on October 19, 1932, at his home in Sea Bright, New Jersey.[4]